Contacts of the helix formed by residues 209 - 214 (chain A) in PDB entry 5DO9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 209 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLY* 3.6 23.1 - - - +
49A GLU* 4.8 3.0 + - - -
183A ARG* 4.1 19.0 - - - +
185A PRO* 5.7 2.9 - - - +
186A THR 4.2 5.4 + - - +
207A GLY 3.8 0.2 - - - -
208A GLY* 1.3 90.6 + - - +
210A ARG* 1.3 68.3 + - - +
211A SER* 4.5 4.7 - - - +
212A GLU* 3.0 16.1 + - + +
213A ARG* 3.4 5.0 + - - +
240A VAL* 4.3 17.8 - - + +
241A GLU* 3.2 28.0 - - + +
122B ASN* 2.8 47.2 + - - +
123B ILE 6.0 0.2 - - - +
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Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A GLN* 1.3 71.6 - - - +
211A SER* 1.3 65.2 + - - +
212A GLU 2.9 1.2 + - - -
213A ARG* 3.0 32.0 + - - +
214A ARG* 4.1 1.9 + - - +
239A LEU* 3.4 13.1 - - - +
241A GLU* 2.9 29.3 + - + +
242A SER* 3.8 12.1 - - - -
245A GLU* 3.1 37.3 + - - -
250A GLU* 2.9 42.7 + - - +
115B VAL* 6.3 2.9 - - - -
120B GLU* 6.1 0.4 - - - +
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Residues in contact with SER 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A GLN* 3.2 2.0 + - - +
210A ARG* 1.3 78.8 - - - +
212A GLU* 1.3 64.4 + - - +
213A ARG 3.5 0.2 + - - -
214A ARG* 3.3 30.4 + - - +
215A LYS* 4.7 1.1 - - - -
241A GLU* 5.4 1.0 - - - +
120B GLU* 3.5 50.6 + - - -
121B VAL 4.4 1.8 - - - -
122B ASN* 3.5 31.4 + - - +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A THR* 2.6 27.7 + - - -
188A GLY* 2.9 17.0 + - - +
207A GLY* 3.4 28.7 + - - +
208A GLY 4.3 0.9 - - - +
209A GLN* 3.0 11.5 + - - +
211A SER* 1.3 83.5 + - - +
213A ARG* 1.3 62.8 + - - +
215A LYS* 2.6 57.6 + - - +
216A TRP* 3.7 7.1 - - - -
81B GLU* 4.6 1.4 - - - +
122B ASN* 3.3 39.5 + - + +
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A THR* 3.8 23.0 - - - +
48A GLY 4.7 0.2 - - - +
208A GLY 2.8 23.6 + - - +
209A GLN 3.5 8.1 + - - +
210A ARG* 3.0 22.3 + - - +
212A GLU* 1.3 72.6 - - - +
214A ARG* 1.3 65.2 + - - +
215A LYS 3.0 2.2 - - - -
216A TRP* 3.0 49.2 + - + +
217A ILE 4.6 0.7 + - - -
239A LEU* 5.1 0.4 - - - +
241A GLU* 3.5 17.2 + - - -
250A GLU* 2.7 35.4 + - - +
254A LEU* 4.0 32.5 - - - +
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Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ARG 4.1 2.2 + - - +
211A SER* 3.3 19.5 + - - +
213A ARG* 1.3 77.6 - - - +
215A LYS* 1.3 88.8 + - + +
216A TRP 3.5 0.3 + - - -
217A ILE* 3.7 17.0 + - - +
218A HIS* 5.6 0.2 + - - -
81B GLU* 3.9 10.3 + - - +
117B ALA 4.8 5.4 + - - -
118B PRO 3.7 21.5 + - - -
119B ARG* 3.8 7.5 - - - +
120B GLU* 3.2 38.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il